Answer:
Better way to do this is to define both envs and env-a and env-b inside the single dockerfile, like so:
Dockerfile
FROM continuumio/miniconda3
WORKDIR /usr/src/app
#Create scripts to run in env-a and env-b (This is for example; pipelines in your case)
COPY run_env_a.sh /usr/src/app/run_env_a.sh
COPY run_env_b.sh /usr/src/app/run_env_b.sh
# Make the scripts executable
RUN chmod +x /usr/src/app/run_env_a.sh /usr/src/app/run_env_b.sh
# Install samtools in env-a
RUN conda create --name env-a -c bioconda samtools
# Install samtools in env-b
RUN conda create --name env-b -c bioconda samtools
# Run the script in env-a
RUN conda run -n env-a /usr/src/app/run_env_a.sh
# Run the script in env-b
RUN conda run -n env-b /usr/src/app/run_env_b.sh
# This is optional and can be removed to use base conda env generated from base image
# Set the default shell to use env-a
SHELL ["conda", "run", "-n", "env-a", "/bin/bash", "-c"]
# Set the default command to activate env-a
CMD ["conda", "run", "-n", "env-a", "/bin/bash"]
# Set the default command to activate env-a (After this command all commands will automatically run in env-a)
CMD ["conda", "run", "-n", "env-a", "/bin/bash”]
